Team:ETHZ Basel/Achievements/Systems Design
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E. lemming is a special project, because the final product has biological and computer science aspects in equal parts. For this reason, it was decided to connect the wet laboratory and the modeling subteam closely from the very beginning to make the best decisions for the whole project. This process is called interworking: multiple parts interact on each other to create a comprehensive result. | E. lemming is a special project, because the final product has biological and computer science aspects in equal parts. For this reason, it was decided to connect the wet laboratory and the modeling subteam closely from the very beginning to make the best decisions for the whole project. This process is called interworking: multiple parts interact on each other to create a comprehensive result. | ||
- | == Experimental data == | + | == Wet Laboratory: Experimental data == |
=== Bacterial movement === | === Bacterial movement === | ||
<<< how did experiments help to improve the bacterial movement model? write about this here. >>> | <<< how did experiments help to improve the bacterial movement model? write about this here. >>> | ||
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<<< how did experimental data (E. coli) help to create cell detection? write about this here. >>> | <<< how did experimental data (E. coli) help to create cell detection? write about this here. >>> | ||
- | == Parameter evaluation == | + | == Mathematical Modeling: Parameter evaluation == |
=== Modeling insights for wet laboratory === | === Modeling insights for wet laboratory === | ||
Mathematical modeling of biological pathways should never be an end in itself. Instead, mathematical models should be build to give insights into the pathway of interest, which are otherwise hard to obtain, or to speed up experimental work. In this project, a molecular setup for implementation by the wet laboratory was evaluated and resulted in an effort alleviating priority list of BioBrick candidates. [[Team:ETHZ_Basel/Modeling/Evaluation#Insights_for_wet_laboratory|'''Parameter Evaluation: Insights for wet laboratory''']] provide more information about this topic. | Mathematical modeling of biological pathways should never be an end in itself. Instead, mathematical models should be build to give insights into the pathway of interest, which are otherwise hard to obtain, or to speed up experimental work. In this project, a molecular setup for implementation by the wet laboratory was evaluated and resulted in an effort alleviating priority list of BioBrick candidates. [[Team:ETHZ_Basel/Modeling/Evaluation#Insights_for_wet_laboratory|'''Parameter Evaluation: Insights for wet laboratory''']] provide more information about this topic. | ||
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- | == Experimental validation == | + | == Information Processing: Experimental validation == |
Revision as of 14:13, 19 October 2010
Interworking: From computer science to biology and back
E. lemming is a special project, because the final product has biological and computer science aspects in equal parts. For this reason, it was decided to connect the wet laboratory and the modeling subteam closely from the very beginning to make the best decisions for the whole project. This process is called interworking: multiple parts interact on each other to create a comprehensive result.
Wet Laboratory: Experimental data
Bacterial movement
<<< how did experiments help to improve the bacterial movement model? write about this here. >>>
Cell detection
<<< how did experimental data (E. coli) help to create cell detection? write about this here. >>>
Mathematical Modeling: Parameter evaluation
Modeling insights for wet laboratory
Mathematical modeling of biological pathways should never be an end in itself. Instead, mathematical models should be build to give insights into the pathway of interest, which are otherwise hard to obtain, or to speed up experimental work. In this project, a molecular setup for implementation by the wet laboratory was evaluated and resulted in an effort alleviating priority list of BioBrick candidates. Parameter Evaluation: Insights for wet laboratory provide more information about this topic.
Che | LSP1 | LSP2 | [Asp] | [AP] | [anchor] |
---|---|---|---|---|---|
CheY | PIF3 | PhyB | 10^-6 uM | 40 uM | 50 uM |
Modeling insights for information processing
Furthermore, the combined model was used to estimate the reaction time of the network on the red and far-red light pulses and the optimal configuration of the light pulse setup, crucial for the controller design. See Parameter Evaluation: Insights for information processing for more details.
model | tc RL | tc FRL |
---|---|---|
Spiro et al. | 0.2200s | 0.3485s |
Mello & Tu | 0.1380s | 0.3205s |